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  • freebayes_anno
  • freebayes_by_region
  • lancet
  • master default protected
  • multiRG
  • mutect
  • recount
7 results
Created with Raphaël 2.2.021Feb26Dec76543130Nov292823Oct171185225Sep212019181173127Aug2118161032131Jul30282726217330Jun2812replace literal tab with \tlancetlancetfix outputmultiRGmultiRGtemp mutect vcf indx by chrchange flagstat and fastqc, cp indel realign recal bam indexrealigned bam index should be bam.baimore infoadd jobnameadd logpicard mergesam create indexadd picard mergeSam create indexfix output for merge bam by chrmerge bam 2 threadspicard creat indexreplace samtools with Picard MergeSamFiles as Picard can handle the readgrouptemp all index baifix bwa literal TABadd comments on bwa @PG TAB issue, bwa v0.7.16 after fix itspecify bwa version fixing TAB in bam headerfix tmp name for realigning bam files by RGadd figureupdate workflow figupdate the workflow figurefix typo, int indexrealign bam with multiple @RGadd cadd annotation for annovaradd time for pyclone_build_tableupdatepad lancet 300bp to call mutationschange write_tsv to write.tablegatk bam coverage and recount annovar worksfilter by depthlancet and mutect recount bamreadcount worklancet mutect common callsextract annovar worksannovar for lancet mutect workingadd lancet calllocal cores limit2change grepl to startswithrecountrecountmove tumor content in the run blockadd techinical notes for sequenza